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comparison plotwithscale.xml @ 70:39e7294c66e1 draft

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Uploaded 20170614
author fabio
date Wed, 14 Jun 2017 13:57:38 -0400
parents 971bb414cc4f
children a3bfaf944f73
comparison
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69:4935e8a8f0b1 70:39e7294c66e1
15 <regex match="Error" source="both" level="fatal" description="An error has occurred. Please try again." /> 15 <regex match="Error" source="both" level="fatal" description="An error has occurred. Please try again." />
16 </stdio> 16 </stdio>
17 17
18 <command> 18 <command>
19 <![CDATA[ 19 <![CDATA[
20 Rscript $__tool_directory__/plotwithscale.R adjustedpvalue="${adjustedpvalue}" iwtomicsrespdf="${iwtomicsrespdf}" iwtomicssumpdf="${iwtomicssumpdf}" 20 Rscript '$__tool_directory__/plotwithscale.R' adjustedpvalue='${adjustedpvalue}' iwtomicsrespdf='${iwtomicsrespdf}' iwtomicssumpdf='${iwtomicssumpdf}'
21 iwtomicsrdata="${rdata}" 21 iwtomicsrdata='${rdata}'
22 iwtomicstests="${testids}" 22 iwtomicstests='${testids}'
23 iwtomicsselectedfeatures="${featureids}" 23 iwtomicsselectedfeatures='${featureids}'
24 24
25 #set test_subset = '"\\|"'.join( [ str( $e.test ) for $e in $scalesection.thresholdontestscale ] ) 25 #set test_subset = '"\\|"'.join( [ str( $e.test ) for $e in $scalesection.thresholdontestscale ] )
26 test_subset="${test_subset}" 26 test_subset='${test_subset}'
27 #set feature_subset = '"\\|"'.join( [ str( $e.feature ) for $e in $scalesection.thresholdontestscale ] ) 27 #set feature_subset = '"\\|"'.join( [ str( $e.feature ) for $e in $scalesection.thresholdontestscale ] )
28 feature_subset="${feature_subset}" 28 feature_subset='${feature_subset}'
29 #set scale_subset = '","'.join( [ str( $e.scale ) for $e in $scalesection.thresholdontestscale ] ) 29 #set scale_subset = '","'.join( [ str( $e.scale ) for $e in $scalesection.thresholdontestscale ] )
30 scale_subset="c(${scale_subset})" 30 scale_subset='c(${scale_subset})'
31 31
32 testalpha="${plotres.alpha}" 32 testalpha='${plotres.alpha}'
33 average="${plotres.average}" 33 average='${plotres.average}'
34 size="${plotres.size}" 34 size='${plotres.size}'
35 plottype="'${plotres.conditionalplottype.plottype}'" 35 plottype='${plotres.conditionalplottype.plottype}'
36 #if $plotres.conditionalplottype.plottype == 'boxplot': 36 #if $plotres.conditionalplottype.plottype == 'boxplot':
37 #set probs = '","'.join( [ str( $p.prob ) for $p in $plotres.conditionalplottype.probabilitiessection.probabilities ] ) 37 #set probs = '","'.join( [ str( $p.prob ) for $p in $plotres.conditionalplottype.probabilitiessection.probabilities ] )
38 #if $probs != "": 38 #if $probs != "":
39 probs="c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2},${probs})" 39 probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2},${probs})'
40 #else: 40 #else:
41 probs="c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2})" 41 probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2})'
42 #end if 42 #end if
43 #end if 43 #end if
44 44
45 groupby="'${plotsum.conditionalgroupby.groupby}'" 45 groupby='${plotsum.conditionalgroupby.groupby}'
46 #if $plotsum.conditionalgroupby.groupby == "test": 46 #if $plotsum.conditionalgroupby.groupby == "test":
47 summaryalpha="${plotsum.conditionalgroupby.testalphaplot}" 47 summaryalpha='${plotsum.conditionalgroupby.testalphaplot}'
48 only_significant="${plotsum.conditionalgroupby.testonlysig}" 48 only_significant='${plotsum.conditionalgroupby.testonlysig}'
49 #elif $plotsum.conditionalgroupby.groupby == "feature": 49 #elif $plotsum.conditionalgroupby.groupby == "feature":
50 summaryalpha="${plotsum.conditionalgroupby.featurealphaplot}" 50 summaryalpha='${plotsum.conditionalgroupby.featurealphaplot}'
51 only_significant="${plotsum.conditionalgroupby.featureonlysig}" 51 only_significant='${plotsum.conditionalgroupby.featureonlysig}'
52 #end if 52 #end if
53 53
54 >& /dev/null 54 >& /dev/null
55 ]]> 55 ]]>
56 <!-- 56 <!--
199 The complete version can be found in the *R/Bioconductor* package *IWTomics* (see vignette_). 199 The complete version can be found in the *R/Bioconductor* package *IWTomics* (see vignette_).
200 200
201 .. _vignette: https://bioconductor.org/packages/release/bioc/vignettes/IWTomics/inst/doc/IWTomics.pdf 201 .. _vignette: https://bioconductor.org/packages/release/bioc/vignettes/IWTomics/inst/doc/IWTomics.pdf
202 ]]></help> 202 ]]></help>
203 203
204 <citations> 204 <expand macro="citations" />
205 <citation type="bibtex">
206 @ARTICLE{
207 iwt-functional-data,
208 author = {A Pini and S. Vantini},
209 title = {Interval-Wise Testing for functional data},
210 journal = {Journal of Nonparametric Statistics},
211 year = {2017},
212 volume = {29},
213 number = {2},
214 pages = {407-424}
215 }
216 </citation>
217 <citation type="bibtex">
218 @MANUAL{
219 iwtomics,
220 author = {Cremona, Marzia A and Pini, Alessia and Chiaromonte, Francesca and Vantini, Simone},
221 title = {IWTomics: Interval-Wise Testing for Omics Data},
222 note = {R package version 1.0.0},
223 year = {2017}
224 }
225 </citation>
226 </citations>
227 205
228 </tool> 206 </tool>